[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
reading reference bed file:  ref_annot.bed  ...  Done! Total 386135 known splicing junctions.
Load BAM file ...  Done
shuffling alignments ... Done
sampling 5% (586985) splicing reads. 95588 splicing junctions. 90902 known splicing junctions. 4686 novel splicing junctions.
sampling 10% (1173971) splicing reads. 114413 splicing junctions. 105877 known splicing junctions. 8536 novel splicing junctions.
sampling 15% (1760957) splicing reads. 125379 splicing junctions. 113499 known splicing junctions. 11880 novel splicing junctions.
sampling 20% (2347942) splicing reads. 133303 splicing junctions. 118456 known splicing junctions. 14847 novel splicing junctions.
sampling 25% (2934928) splicing reads. 139583 splicing junctions. 122152 known splicing junctions. 17431 novel splicing junctions.
sampling 30% (3521914) splicing reads. 145067 splicing junctions. 125138 known splicing junctions. 19929 novel splicing junctions.
sampling 35% (4108899) splicing reads. 149523 splicing junctions. 127448 known splicing junctions. 22075 novel splicing junctions.
sampling 40% (4695885) splicing reads. 153553 splicing junctions. 129406 known splicing junctions. 24147 novel splicing junctions.
sampling 45% (5282871) splicing reads. 157174 splicing junctions. 131080 known splicing junctions. 26094 novel splicing junctions.
sampling 50% (5869857) splicing reads. 160301 splicing junctions. 132536 known splicing junctions. 27765 novel splicing junctions.
sampling 55% (6456842) splicing reads. 163213 splicing junctions. 133855 known splicing junctions. 29358 novel splicing junctions.
sampling 60% (7043828) splicing reads. 165849 splicing junctions. 135017 known splicing junctions. 30832 novel splicing junctions.
sampling 65% (7630814) splicing reads. 168218 splicing junctions. 136010 known splicing junctions. 32208 novel splicing junctions.
sampling 70% (8217799) splicing reads. 170300 splicing junctions. 136871 known splicing junctions. 33429 novel splicing junctions.
sampling 75% (8804785) splicing reads. 172239 splicing junctions. 137620 known splicing junctions. 34619 novel splicing junctions.
sampling 80% (9391771) splicing reads. 174079 splicing junctions. 138385 known splicing junctions. 35694 novel splicing junctions.
sampling 85% (9978756) splicing reads. 175685 splicing junctions. 139044 known splicing junctions. 36641 novel splicing junctions.
sampling 90% (10565742) splicing reads. 177173 splicing junctions. 139627 known splicing junctions. 37546 novel splicing junctions.
sampling 95% (11152728) splicing reads. 178523 splicing junctions. 140140 known splicing junctions. 38383 novel splicing junctions.
sampling 100% (11739714) splicing reads. 179686 splicing junctions. 140590 known splicing junctions. 39096 novel splicing junctions.